December 11, 2025 Webinar
Integrating Transcriptomics and Lineage Information for Differentiation Trajectory Inference in Single Cell Studies
Juan Xie, PhD
Abstract:
Single-cell RNA sequencing (scRNA-seq) and T cell receptor sequencing (scTCR-seq) provide complementary information for studying T cell differentiation: scRNA-seq captures functional phenotypes, while scTCR-seq encodes clonal lineage. Traditional trajectory inference methods rely solely on transcriptomics and may obscure clonal-level heterogeneity. I will present LRT, a computational framework that integrates scRNA-seq and scTCR-seq to reveal clonal differentiation trajectory heterogeneity. LRT first constructs global trajectories from transcriptomic profiles, then incorporates TCR sequence and phenotypic information to identify clonotype clusters exhibiting distinct differentiation biasedness. The framework provides a full analysis workflow-including preprocessing, clonotype clustering, trajectory biasedness evaluation, and clonotype cluster characterization-and is implemented as an R package with two interactive Shiny apps. Applications to viral infection datasets demonstrate that LRT uncovers biologically meaningful clonal substructures that cannot be detected from scRNA-seq alone.
Short Bio:
Juan Xie, PhD is a research associate in the Department of Epidemiology and Public Health at the University of Maryland, Baltimore. Her research focuses on statistical and computational methods for single cell and spatial omics data, with application to cancer immunology. She received her PhD in Biostatistics from The Ohio State University in 2025.
Hope to see you at the webinar!